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- PDB-3rx6: Crystal structure of Polarity Suppression protein from Enterobact... -

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Basic information

Entry
Database: PDB / ID: 3rx6
TitleCrystal structure of Polarity Suppression protein from Enterobacteria phage P4
ComponentsPolarity suppression protein
KeywordsTranscription Regulator / All alpha protein / transcription termination inhibitor / Rho binding / capsid decoration protein of bacteriophage P4 / Transcription termination inhibition / Transcription terminator Rho helicase / Enterobacteria phage P4 capsid
Function / homology
Function and homology information


symbiont-mediated activation of of host transcription
Similarity search - Function
Phage polarity suppression protein monomer / Bacteriophage P4, Psu, polarity suppression protein / Phage polarity suppression protein (Psu) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / IODIDE ION / Polarity suppression protein
Similarity search - Component
Biological speciesEnterobacteria phage P4 (virus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.039 Å
AuthorsBanerjee, R. / Nath, S. / Khamrui, S. / Sen, R. / Sen, U.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The first structure of polarity suppression protein, Psu from enterobacteria phage P4, reveals a novel fold and a knotted dimer
Authors: Banerjee, R. / Nath, S. / Ranjan, A. / Khamrui, S. / Pani, B. / Sen, R. / Sen, U.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polarity suppression protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8434
Polymers21,3931
Non-polymers4503
Water3,891216
1
A: Polarity suppression protein
hetero molecules

A: Polarity suppression protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6858
Polymers42,7862
Non-polymers8996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4540 Å2
ΔGint-48 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.750, 148.750, 63.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-298-

HOH

21A-307-

HOH

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Components

#1: Protein Polarity suppression protein / Amber mutation-suppressing protein


Mass: 21393.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P4 (virus) / Gene: psu / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P05460
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7.5% PEG 6000, 5% glycerol, 0.5mM DTT, 300mM NaCl, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2009 / Details: Osmic maxflux
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.039→47.039 Å / Num. obs: 22442 / % possible obs: 98.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.052 / Net I/σ(I): 13.4
Reflection shellResolution: 2.039→2.11 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 13.4 / Num. unique all: 22442 / Rsym value: 0.052 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.039→47.039 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8605 / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.69 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1970 8.78 %RANDOM
Rwork0.1921 ---
obs0.1945 22442 97.69 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.593 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 136.95 Å2 / Biso mean: 36.5319 Å2 / Biso min: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.4504 Å20 Å20 Å2
2--0.4504 Å2-0 Å2
3----0.9009 Å2
Refine analyzeLuzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.039→47.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 10 216 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071505
X-RAY DIFFRACTIONf_angle_d0.9282031
X-RAY DIFFRACTIONf_chiral_restr0.06225
X-RAY DIFFRACTIONf_plane_restr0.004269
X-RAY DIFFRACTIONf_dihedral_angle_d13.606568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0388-2.11170.32281810.24911905208692
2.1117-2.19630.26281950.20481972216796
2.1963-2.29620.22891890.19591997218697
2.2962-2.41730.23621910.18972033222498
2.4173-2.56870.22921990.2032042224198
2.5687-2.7670.27511980.20262040223899
2.767-3.04540.20932000.18172073227399
3.0454-3.4860.2052000.18182079227999
3.486-4.39150.1882050.168521382343100
4.3915-47.05140.20762120.2072193240598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30260.1812-0.13960.1712-0.08970.08770.01930.29450.1791-0.0961-0.3724-0.31570.06030.10750.08920.10510.10460.00080.2650.08750.188329.512559.978817.8958
20.6669-0.2571-0.90830.95390.4511.27120.13970.0814-0.07450.2465-0.09690.05850.0538-0.1842-0.04460.21010.09690.01420.20670.01960.161519.457861.117121.4606
30.28420.1908-0.15060.6369-0.0880.61490.07570.18060.0119-0.13970.02950.03670.1864-0.2325-0.04240.20450.0552-0.00190.19780.01690.15524.851462.748225.1742
41.2472-0.403-0.77450.36450.28372.88950.1302-0.17320.2841-0.21160.2116-0.04060.60760.0975-0.28080.24810.00130.03310.17960.02640.1341-11.184565.80228.3804
50.5366-0.3660.6532.21981.3832.48170.6252-0.21330.83780.1459-0.364-0.1860.2587-0.4127-0.28940.0774-0.02460.06640.58650.02760.297-19.412864.353223.3702
62.6563-0.2137-0.80522.84570.44761.69870.10220.7298-0.2257-0.2344-0.0627-0.07030.571-0.1930.00840.2485-0.0601-0.01550.24310.06030.1968-8.203758.582320.8163
70.58390.16360.30530.7736-0.06640.65860.19780.0464-0.0921-0.0842-0.05260.10280.32950.0946-0.09430.20330.0984-0.0240.1652-00.142914.026753.817223.0192
81.34330.4997-0.41781.4408-0.78191.59380.17760.2341-0.143-0.2344-0.5557-0.4146-0.24240.42760.18440.28350.1903-0.01670.31950.04550.285737.558751.318523.2898
92.9358-0.4463-0.79433.441-1.13920.68190.37670.57770.1641-0.1561-0.7792-0.3798-0.25590.35390.26860.280.10390.04110.35930.18730.401148.697149.906426.0433
100.7501-0.78830.21340.7967-0.2730.07570.25150.69230.0891-0.5818-0.476-0.27680.28640.42170.1130.32770.19910.02130.39730.05440.277951.258236.460427.8674
110.4373-0.49091.04525.21610.32952.984-0.0507-0.07670.0271-0.2563-0.44620.0062-0.1089-0.31580.41860.86780.21340.07920.5106-0.03020.436346.812127.208619.3788
122.3531-0.4382.1244.0028-1.17752.0715-0.1564-0.5113-0.0632-0.19910.1927-0.61740.2141-0.46940.05320.40040.1895-0.0010.3699-0.14220.465141.642930.174825.416
131.2172-2.085-1.80844.00093.11152.8349-0.1975-0.0018-0.44650.5525-0.32070.41790.34140.01520.25090.28430.1124-0.00490.2301-0.02980.256241.382835.480234.9465
141.6712-0.6454-1.27480.53360.00271.8901-0.4826-0.08760.2870.40080.0472-0.2808-0.0367-0.09040.27880.40250.1722-0.10860.248-0.05280.148341.114347.274642.7505
150.29870.00650.14740.6505-0.05320.0731-0.3410.11950.6566-0.065-0.0304-0.6832-0.28760.12750.3480.38790.0711-0.16520.30080.01740.563937.103759.108832.6955
162.0385-0.01360.24131.36320.27110.5057-0.1073-0.63310.57740.5180.19590.24040.198-0.1612-0.04850.16710.1406-0.06210.19070.00750.099321.244656.864631.0366
172.0987-0.82510.16841.4609-0.63360.83780.2045-0.2904-0.90780.383100.46760.16660.1371-0.22080.51850.06110.00550.25180.04090.42315.485444.77221.7534
180.45470.4441-0.32180.4677-0.53332.32540.21050.09720.2097-0.31710.52560.22560.45150.1844-0.44310.41480.0174-0.120.2318-0.10410.32511.402649.237612.5999
193.14532.4445-1.2162.7099-0.78861.6561-0.00850.46610.12590.08820.46430.27430.0607-0.3751-0.39930.21310.0773-0.00780.31280.0340.21980.144157.658712.0122
205.43191.3814.41587.5524.06065.034-0.9171-0.81991.4750.3936-0.4313-0.397-0.5675-0.13261.00880.42780.015-0.3640.30850.11090.6245-3.391867.452711.0109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:11)A4 - 11
2X-RAY DIFFRACTION2(chain A and resid 12:18)A12 - 18
3X-RAY DIFFRACTION3(chain A and resid 19:32)A19 - 32
4X-RAY DIFFRACTION4(chain A and resid 33:40)A33 - 40
5X-RAY DIFFRACTION5(chain A and resid 41:46)A41 - 46
6X-RAY DIFFRACTION6(chain A and resid 47:56)A47 - 56
7X-RAY DIFFRACTION7(chain A and resid 57:77)A57 - 77
8X-RAY DIFFRACTION8(chain A and resid 78:87)A78 - 87
9X-RAY DIFFRACTION9(chain A and resid 88:92)A88 - 92
10X-RAY DIFFRACTION10(chain A and resid 93:107)A93 - 107
11X-RAY DIFFRACTION11(chain A and resid 108:114)A108 - 114
12X-RAY DIFFRACTION12(chain A and resid 115:120)A115 - 120
13X-RAY DIFFRACTION13(chain A and resid 121:128)A121 - 128
14X-RAY DIFFRACTION14(chain A and resid 129:138)A129 - 138
15X-RAY DIFFRACTION15(chain A and resid 139:147)A139 - 147
16X-RAY DIFFRACTION16(chain A and resid 148:165)A148 - 165
17X-RAY DIFFRACTION17(chain A and resid 166:174)A166 - 174
18X-RAY DIFFRACTION18(chain A and resid 175:179)A175 - 179
19X-RAY DIFFRACTION19(chain A and resid 180:185)A180 - 185
20X-RAY DIFFRACTION20(chain A and resid 186:190)A186 - 190

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